Mass spectrometry has risen to prominence in the life sciences because it is indispensable for identifying and quantifying structural and functional modifications to proteins. However, only a small fraction of the information potentially available can be accessed by current instruments. In high-throughput, bottom-up proteomics experiments, only about 16% of peptides are identifiable with the best currently available technology.
The speed, resolution and high mass accuracy of modern mass spectrometers have revolutionized many fields, such as proteomics, for example to determine the location of fragile post-translational modifications that control most cellular processes. However, accurate identification and quantitation of phosphorylation sites remain a major challenge in proteomics. The key weakness with mass spectrometry for phospho-proteomics lies in the methods used to induce fragmentation, because phosphoryl bonds are among the most labile chemical bonds in proteins and are lost in complex ways by current collision-based fragmentation approaches. An alternative fragmentation methodology called electron capture dissociation (ECD) is well established to produce exceptional spectra of phosphopeptides, but is currently feasible only in expensive FTICR mass spectrometers. The fundamental limitation to ECD is providing enough low-energy electrons to efficiently fragment peptides.